Mercurial > repos > imgteam > 2d_feature_extraction
changeset 6:5bc8cdc17fd0 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
| author | imgteam |
|---|---|
| date | Wed, 24 Apr 2024 08:11:39 +0000 |
| parents | 2436a8807ad1 |
| children | |
| files | 2d_feature_extraction.py 2d_feature_extraction.xml |
| diffstat | 2 files changed, 9 insertions(+), 8 deletions(-) [+] |
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--- a/2d_feature_extraction.py Thu Apr 04 15:23:23 2024 +0000 +++ b/2d_feature_extraction.py Wed Apr 24 08:11:39 2024 +0000 @@ -1,9 +1,9 @@ import argparse +import giatools.io import numpy as np import pandas as pd import skimage.feature -import skimage.io import skimage.measure import skimage.morphology import skimage.segmentation @@ -57,9 +57,9 @@ raw_image = None if args.raw_file is not None: - raw_image = skimage.io.imread(args.raw_file.name) + raw_image = giatools.io.imread(args.raw_file.name) - raw_label_image = skimage.io.imread(label_file) + raw_label_image = giatools.io.imread(label_file) df = pd.DataFrame() if label_file_binary: @@ -124,4 +124,4 @@ df['convexity'] = area / (perimeter * perimeter) del df['it'] - df.to_csv(out_file, sep='\t', line_terminator='\n', index=False) + df.to_csv(out_file, sep='\t', lineterminator='\n', index=False)
--- a/2d_feature_extraction.xml Thu Apr 04 15:23:23 2024 +0000 +++ b/2d_feature_extraction.xml Wed Apr 24 08:11:39 2024 +0000 @@ -2,7 +2,7 @@ <description>with scikit-image</description> <macros> <import>creators.xml</import> - <token name="@TOOL_VERSION@">0.14.2</token> + <token name="@TOOL_VERSION@">0.18.1</token> <token name="@VERSION_SUFFIX@">0</token> </macros> <creator> @@ -17,9 +17,10 @@ </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement> - <requirement type="package" version="0.23.4">pandas</requirement> - <requirement type="package" version="1.15.4">numpy</requirement> - <requirement type="package" version="0.15.1">tifffile</requirement> + <requirement type="package" version="2.2.2">pandas</requirement> + <requirement type="package" version="1.23.3">numpy</requirement> + <requirement type="package" version="2020.10.1">tifffile</requirement> + <requirement type="package" version="0.1">giatools</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[